Can you do convex hull on ChimeraX?
Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming
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@cgl.ucsf.edu> wrote:
Hi dear ChimeraX-Users and developers,
Is ChimeraX available for drawing the convex hull of protein structures?
Best, Tianming
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@cgl.ucsf.edu> À: "Tianming Qu" <tqu@fsu.edu> Cc: "chimerax-users" <chimerax-users@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@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] > wrote: Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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/co... | https://git.app.uib.no/reuter-group/protrusions_msc_florian/-/tree/master/co... ] Best, Thibault. De: "Thibault TUBIANA" <thibault.tubiana@i2bc.paris-saclay.fr> À: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu>, "Elaine Meng" <meng@cgl.ucsf.edu> Cc: "Tianming Qu" <tqu@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@cgl.ucsf.edu> À: "Tianming Qu" <tqu@fsu.edu> Cc: "chimerax-users" <chimerax-users@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@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] > wrote: Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tianming, The SciPy package that ChimeraX includes has a convex hull function so I wrote a little code to use it and display the convex hull surfaces. https://rbvi.github.io/chimerax-recipes/convex_hull/convex_hull.html <https://rbvi.github.io/chimerax-recipes/convex_hull/convex_hull.html> Here is a photosystem 1 shown as a solvent excluded molecular surface (6 million triangles) compared to convex hull surfaces for each protein (3000 triangles) giving it a mineral look. Tom
On Oct 7, 2022, at 6:49 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi dear ChimeraX-Users and developers,
Is ChimeraX available for drawing the convex hull of protein structures?
Best, Tianming _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (4)
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Elaine Meng -
Thibault TUBIANA -
Tianming Qu -
Tom Goddard