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

[Thibault TUBIANA]

Sorry, the mail was sent early... 

Link : [ https://reuter-group.github.io/peprmint/pepr2vis | https://reuter-group.github.io/peprmint/pepr2vis ] 
Also, one of our previous internship student has developped a convexhull pluggin for Chimera (not chimeraX, maybe it can be adapted....) : [ https://git.app.uib.no/reuter-group/protrusions_msc_florian/-/tree/master/convexhull_plugin | https://git.app.uib.no/reuter-group/protrusions_msc_florian/-/tree/master/convexhull_plugin ] 

Best, 
Thibault. 


De: "Thibault TUBIANA" <thibault.tubiana at i2bc.paris-saclay.fr> 
À: "ChimeraX Users Help" <chimerax-users at cgl.ucsf.edu>, "Elaine Meng" <meng at cgl.ucsf.edu> 
Cc: "Tianming Qu" <tqu at fsu.edu> 
Envoyé: Dimanche 9 Octobre 2022 11:17:38 
Objet: Re: [chimerax-users] Can you do convex hull on ChimeraX? 

Hi! 

just adding something to this, my previous postdoc team have developped a webinterface to visualise convexhull with molstar. 
Not the best of course because it's not chimeraX, but you might want to have a look for ChimeraX 



De: "Elaine Meng via ChimeraX-users" <chimerax-users at cgl.ucsf.edu> 
À: "Tianming Qu" <tqu at fsu.edu> 
Cc: "chimerax-users" <chimerax-users at cgl.ucsf.edu> 
Envoyé: Vendredi 7 Octobre 2022 17:42:23 
Objet: Re: [chimerax-users] Can you do convex hull on ChimeraX? 

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 < [ mailto:chimerax-users at cgl.ucsf.edu | 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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