[Chimera-users] [chimera-dev] icosahedron with a T number

[Wei Zhang]

Elaine,

Thank you. Yes. I played with the "cage builder" last night and liked it. I
was able to build a T=13 lattice manually (h,k=3,1). But it is too
difficult for larger h or k values.

I think probably i can write a .bild file with a certain object  (eg. a
sphere) appears at the center of each pentamer to help visualization.

Is there a way to write out a file that contains the centers coordinates of
each hexagon or pentagon?

Thanks!

Wei

On Fri, Apr 10, 2020 at 3:05 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Wei,
> In the mesh from "hkcage", a pentagon edge might also be a hexagon edge.
> So there is no option to make hexagons a different color than the
> pentagons, if that's what you meant, sorry.
>
> There is another tool "Cage Builder" (in menu under Tools... Higher-Order
> Structure) that lets you build up pentagons and hexagons manually.  They
> have separate edges and are automatically different colors from each other,
> but it may be too difficult to build the whole thing that way.  Also, there
> isn't an option to control the colors of the hexagons and pentagons; the
> pentagons are always orange and the hexagons blue.
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html
> >
>
> Best,
> Elaine
>
> > On Apr 10, 2020, at 9:06 AM, Wei Zhang <zhangwei at umn.edu> wrote:
> >
> > Hi Elaine,
> >
> > I am able to use hkcage and build a spherical sphere with pentagons and
> hexagons. Is there a way to color those pentagons differently?
> >
> > Thank you,
> >
> > Wei
> >
> > On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei at umn.edu> wrote:
> > Hi Elaine,
> >
> > Thank you for the quick reply and the instructions.
> > I will use the other email address next time.
> >
> > Best regards,
> >
> > Wei
> >
> > On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Wei,
> >
> > Take a look at the "hkcage" command if you want hexagons and pentagons
> instead of triangles.  You give it the h and k values which are related to
> T number by the equation shown in that page:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html>
> >
> > For this kind of question (next time) you probably want the
> chimera-users at cgl.ucsf.edu mailing list, not chimera-dev which is more
> for programming questions.
> >
> > Thank you for the good wishes -- you stay safe too!
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Apr 9, 2020, at 4:21 PM, Wei Zhang <zhangwei at umn.edu> wrote:
> > >
> > > Hello,
> > >
> > > I have been playing with the icosahedron utility in Chimera. I really
> like this feature, especially with the sphere factor.
> > >
> > > The current routine uses a subdivision factor to represent the number
> of triangles on an icosahedral surface. However this lattice is not the
> same as we see in icosahedral viruses, which use a T number to designate
> symmetry. With a subdivision number, there are always hexamers on any edge
> of the icosahedron, whereas in the virus structure this is not the case.
> > >
> > > I am wondering if Chimera has an utility that can use the T number as
> the basis for building an icosahedron surface.
> > >
> > > Thank you.
> > >
> > > Hope everything is going well and stay safe!
> > >
> > > Wei
> >
> > _______________________________________________
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>
>
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