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

[Wei Zhang]

Tom,

Boy, there is so much to learn from Chimera!

I was able to follow the sequence of the commands listed in your email and
produce colored facets of a pentagon and a hexagon.

Thank you for your help!

Wei

On Fri, Apr 10, 2020 at 6:50 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Wei,
>
>   Did you see the Chimera example of using hkcage to color a virus?
>
> https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html
>
> It has a script markhidden.py.  I just tried it with commands "hkcage 3 1"
> and "open ~/Downloads/markhidden.py".  That script put markers at all the
> hexamer and pentamer centers.  I made them bigger with "vdwdefine 3 #1".
> But it also put a bunch of additional undesired markers on the icosahedron
> edges (where the pentagons and hexagons are folded).  I could select by
> hand (ctrl click, and shift ctrl click) and delete the undesired markers
> (menu Actions / Atoms / Delete).  Another thing I tried is fattening up the
> mesh lines with "meshmol #0 1" and colored the fattened lines "color orange
> #2".  Then I tried another tool Volume Tracer (Chimera menu Tools / Volume
> Data / Volume Tracer), selected by hand the vertices of my orange mesh
> around a hexagon, and used Volume Trace menu Features / Surfaces and
> pressed the create button to make some color planes for a hexagon and a
> pentagon.
>
>   So there are lots of Chimera tools that can help you manually do this
> stuff, but it is pretty tedious.
>
> Tom
>
>
>
> On Apr 10, 2020, at 1:16 PM, Wei Zhang <zhangwei at umn.edu> wrote:
>
> 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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