[chimerax-users] Can you do convex hull on ChimeraX?

[Elaine Meng]

Hi Tianming,
Sorry, ChimeraX does not include calculation of the Voronoi diagram or convex hull of a structure.

I thought maybe a molecular surface calculated with very large probe radius might produce something similar, but this is not the normal usage of the command and is VERY slow.  This took maybe one minute on a medium-sized protein:

surface probe 10

...and this took several minutes on 1r3j:

surface probe 25

Also I'm not sure the result would be adequate for your purposes.  Picture of the probe-25 test attached. By default it makes a separate surface for each chain, although you can use command options to put all the chains into one surface.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Oct 7, 2022, at 6:49 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi dear ChimeraX-Users and developers,
>  
> Is ChimeraX available for drawing the convex hull of protein structures?
>  
> Best,
> Tianming

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